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Analysis of the aclB gene in a hot spring: a non-16S rRNA gene example

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Revision as of 14:55, 13 August 2009 by Westcott (Talk | contribs) (Were all of the OTUs recovered from the hot spring?)

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Although the majority of community analyses are done with 16S rRNA gene sequences, it is possible to use mothur for any gene using nucleotide or amino acid sequences. In this tutorial, we will use the mothur tools to re-analyze ATP citrate lyase (aclB) gene sequences from Coffee Pots Hot Spring originally published by Hall et. al. and compare the two approaches to analysis. In the original analysis, OTUs were defined by PHRAP assembly, the identity of the sequences was determined by phylogenetic analysis, and the aclB sequences from seven sites were compared using the pairwise dissimilarity statistic (Fst) implemented in Arlequin. You can download all of the files needed for this analysis (aclB.zip) or generate your own by following the instructions below.

NOTE: The sample names used in the paper and in this tutorial are different (numbers in COF names are temperature in C):

  • COF_39.3 = 257CP
  • COF_51.4 = 258CP
  • COF_51.9 = 259CP
  • COF_57.7 = 260CP
  • COF_61.7 = 261CP
  • COF_65.7 = 3Y35
  • COF_74.1 = 263CP


Getting Started

I used ARB to align and edit my sequences and to make distance matrices and trees. A good ARB tutorial is availalbe here

Translating Nucleotide Sequences

It is easy to translate nucleotide sequences to amino acid sequences in ARB, but it must be done before aligning either set of sequences:

  1. Mark all of the sequences
  2. In the ARB_NT window, Sequence → Perform Translation
  3. In the window that pops up, choose:
    • Source Alignment = ali_new
    • Destination Alignment = ????? (ARB will make a new alignment database)
    • How to select codon table and start position = use settings below (same for all species)
    • Start Position = 1
    • Codon Table = (1) Standard Code
    • Check "Translate all data"
    • Click Translate!
    • In the window that pops up, choose "Create"


ARB won't translate the nucleotide sequences correctly if they are aligned, so it is important to perform a translation first and then align your nucleotide and amino acid sequences separately. To check your translation, choose the "ali_new_pro" from the alignment box. Your amino acid sequences should match the alignment published by Campbell et al.


Making an Alignment

Unfortunately there is not an automated way to generate an alignment for the aclB sequences, so the sequences were hand-aligned. A good alignment was obtained with about half of the sequences and then the remaining sequences were aligned using the Fast Aligner in ARB:

  1. Mark and select all unaligned sequences and open the ARB_EDIT window
  2. Go Edit → Integrated Aligners.
  3. In the window that pops up, choose:
    • Aligner = Fast Aligner
    • Align what? = Selected Species
    • Reference = Species by name (input an aligned sequence name in box)
    • Range = Whole sequence
    • Hit Go!

Amino acid sequences can be aligned in the exact same way. It is always a good idea to check the alignments by hand again after the automated alignment.


Making a Filter

A filter was made to mask out the “loose ends” of all the sequences in order to compare only overlapping regions:

  1. In the ARB_NT window, Go SAI → Create SAI Using... → Filter by base frequency
  2. In the window that pops up, choose "ali_new"
  3. Go Config → Column filter
  4. In the window that pops up, change the “start at column” to 864 and the “stop at column” to 1244
  5. Go Calculate → Column filter
  6. Go File → Export filter. Press "Export" to export the filter under the name "aclB_864_1244". Now press "Close". Press "Quit" in the window with the purple background

This filter masks out all of the positions outside of the input range, which in this case, was only about 30 nucleotides. Any sequences that did not have complete sequence data in this range were removed from further analysis. This was repeated for the amino acid sequences (just select your amino acid alignment when prompted), though the only regions masked out were those present in other sequences used for making a tree.


Making a Distance Matrix

Finally, a phylip-formatted distance matrix was made:

  1. In the ARB_NT window, go Sequence → Compare sequences using Distance Matrix
  2. In the window that pops up, choose:
    • Which species? = marked
    • Alingment = ali_new
    • Filter = aclB_864_1244
  3. You may or may not want to select a "Correction", but for this example we will just look at the raw distance.
  4. Press the "Calculate Full Matrix" button
  5. Press the "Save Matrix" button
  6. In the window that opens change the file name from "infile" to "aclB.dist" and press "Save". If it gives you an error message that says, "No valid tree given to sort matrix (using default database order)" just ignore it.

You can make a distance matrix for the amino acid sequences by choosing your amino acid alignment and filter instead.


Making a Phylogenetic Tree

We will use a few representative sequences from the Epsilonproteobacteria and Aquificales with the mouse gene as an outgroup to make a tree, as was done in the original analysis. These sequences were downloaded from NCBI in fasta format, imported into ARB, and aligned using the same strategy used above. A maximum likelihood tree was made:

  1. Mark all of the sequences to be used in the tree using the Search and Query window ("Search" button at the top of the ARB_NT window). The NCBI sequences will be marked upon import. Our aclB genes can be marked by searching for them with the wildcard (*).
    • Enter *p2* in the search field with the 'name' option selected.
    • Hit Search. A list of sequence names will appear in the 'Hitlist' box
    • Go More Functions → Mark Listed Species, Don't Change Rest
    • Repeat search for *p3*
  2. Go Tree → Build tree from sequence data → Maximum Likelihood methods → AxML + FastdnaML
    Phylogenetic tree from the original paper
  3. In the window that pops up, choose:
    • Species = Marked
    • Alignment = ali_atpcl
    • Filter = aclB_864_1244
    • Compression = vertical gaps
    • Select Program to use = FastdnaML
    • Use Quickadd = Yes
    • Hit GO!
  4. Another window will pop up to indicate the calculation is running.

An amino acid-based maximum likelihood tree can be made by choosing Phylip PROML instead of FastdnaML. I ran it with all of the default options.

The nucleotide tree took ~ 12 hours to finish on my computer. When it is done, it will be read in to the ARB tree menu with the prefix of "tree_fml_". The tree should look similar to the one on the right with a clade of Epsilonproteobacteria in the most basal position, an Aquificales clade in a more derived position, and all of the aclB in a large clade with the Sulfurihydrogenibum sequence.


OTU-based Approaches

How many OTUs are there?

The following commands will load the distance matrix and cluster the aclB sequences into OTUs using the furthest neighbor algorithm (default). Repeat for the aclB_aa.dist file.

mothur > read.dist(phylip=aclB.dist)
mothur > cluster()

The cluster command generated three files: aclB.sabund (species abundance file), aclB.rabund (rank abundance file), and aclB.list (a list of sequences in each OTU) for the entire dataset. Here are the first two columns of the aclB.fn.list and aclB_aa.fn.list files, which show the distance level and number of OTUs for the total dataset:

Nucleotide Sequences                  Amino Acid Sequences
unique		208                     unique		63
0.00		148                     0.01            51
0.01		 44                     0.02            14
0.02		 25                     0.03            10
0.03		 15                     0.04             8
0.04		  8                     0.05             6
0.05		  5                     0.06             4
0.06		  3                     0.07             3
0.07		  1                     0.08             2
                                        0.11             1


In the original analysis, 11 unique OTUs were defined by PHRAP assembly of the nucleotide sequences. Using mothur, we can see that this is equivalent to nucleotide OTUs defined at a distance somewhere between 0.05 and 0.06 (approximately genus level). Other important observations can be made from just this first step:

  • All of the nucleotide sequences are > 93% similar and amino acid sequences > 89% similar as only one OTU is formed at distances of 0.07 and 0.11, respectively.
  • The number of input sequences is less than the number of unique sequences for both nucleotide and amino acid sequences, so many of the sequences must be identical (307 input vs. 208 unique for nucleotide sequences, 63 unique for amino acid sequences).
  • There are more nucleotide OTUs than amino acid OTUs at many distance level, which indicates some differences in the nucleotide sequences do not translate into differences in the protein sequences (synonymous changes).
  • There is agreement between this data and the range of percentage similarity for the amino acid sequences (88.3 – 100%) reported in the original paper.


Next, we can identify the OTUs present in each sample by reading the .list files into memory and indicating which sequences belong to each sample with the .groups files.

mothur > read.otu(list=aclB.fn.list, group=aclB.groups)

The individual .rabund files (e.g. aclB.fn.257CP.rabund) and .shared file will be needed later to make rarefaction curves and heatmaps.

Were all of the OTUs recovered from the hot spring?

Rarefaction curves are a good way to visualize the extent to which the richness of the environment was represented in the sample. Mothur can rarefy both individual samples and a total dataset with the rarefaction.single command. Let’s look at both, starting with the individual samples:


mothur > read.otu(rabund=aclB.fn.263CP.rabund)
mothur > rarefaction.single(freq=10)

The read.otu command reads each separate OTU file into memory, so this must be repeated for all seven .rabund files for both nucleotide and amino acid sequences. Adding the freq option to the rarefaction command outputs more lines of data and allows us to make a smoother curve, a good option when you are working with less than 100 sequences.


Individual rarefaction curves for A) nucleotide and B) amino acid OTUs a distance of 0.02.


From the graphical representation of the mothur file, we can see that three samples have reached asymptotic saturation - 260CP for nucleotide sequences and 261CP & 263CP for amino acid sequences - and are a reasonable estimate of diversity found in the environment. The remaining samples have varying degrees of saturation from nearing an asympotote (260CP amino acid curve) to nearly linear (both 257CP curves). Since these do not represent the diversity seen in nature, the remaining analyses we perform with them should be interpreted with caution.


All of the sequences can be rarefied using the same commands with the combined .list file (repeat for amino acid file):

mothur > read.otu(list=aclB.fn.list)
mothur > rarefaction.single(freq=10)
Rarefaction curve for all of the sequences obtained from Coffee Pots hot spring for a distance of 0.02.



The amino acid curve is closer to reaching an asymptote than the nucleotide curve, but there are likely more aclB nucleotide and amino acid sequences in Coffee Pots hot spring that were not retrieved.

How are the OTUs distributed in the hot spring?

In the original analysis, the authors noted, "the distribution of phylotypes among samples was widespread, except for phylotype G6, which was found only in sample COF_51.9 (259CP here)", but no formal description of OTU distributional patterns was made. With mothur, we can graphically represent the OTU distribution with a heatmap and compare samples with venn diagrams.


Heatmaps

The following commands will produce a heatmap.bin (.svg file) for every distance (repeat with amino acid files):

mothur > read.otu(list=aclB.fn.list, group=aclB.groups)
mothur > heatmap.bin(scale=linear)


Heatmaps for A) nucleotide sequences and B) amino acid sequences for a distance of 0.02 (no scaling transformation)


We can make a couple observations from this representation:

  • All of the samples, even those with very few sequences, share a set of both nucleotide and amino acid OTUs and they are some of the most abundant OTUs in each sample. This might represent a core population of ATP citrate lyase enzymes that are the best-adapted with other, possibly deleterious, forms represented at a lower abundance throughout the spring.
  • Each sample has fewer amino acid OTUs than nucleotide OTUs, again underscoring the fact that some of the sequence diversity represents synonymous changes.


Venn Diagrams

It is also possible to make comparisons of community composition for 2-3 samples using a Venn diagram. For this tutorial, we will compare the samples that reached a plateau in the rarefaction curves (260CP, 261CP, 263CP). I had to make a new distance matrix and .groups file with only the samples I wanted to analyze for the venn command to work:

mothur > read.dist(phylip=aclB_venn.dist)
mothur > cluster()
mothur > read.otu(list=aclB_venn.fn.list, group=aclB_venn.groups)
mothur > venn()


Venn Diagram for A) nucleotide and B) amino acid sequences for a distance of 0.02 (not to scale)




Here we can see, like in the heatmap, there is quite a bit of overlap between samples in both nucleotide and amino acid sequences - 260CP and 263CP don't have any unique OTUs and 261CP has only 3 unique nucleotide OTUs and 2 unique amino acid OTUs.







Hypothesis-Testing Approaches

Originally, community differences were analyzed using the pairwise dissimilarity index (Fst) in Arlequin. The Fst index calculates the distribution of genetic variation between two samples and can take any value between 0 and 1. A 0 indicates the genetic variation between samples is equal to the genetic variation within samples (in other words, no difference between samples) and 1 indicates all genetic variation is between samples (in other words, completely different communities). As the table below shows, most pairwise comparisons had low, but significant, Fst values (0.18 - 0.23) and the comparisons made with COF_61.7 (261CP) and COF65.7 (3Y35) had high, significant Fst values (0.34 - 0.60).


Results from the pairwise comparison done in the original paper using Arlequin


In mothur, we can make global and pairwise comparisons based on distance (libshuff) and phylogeny-associated information (parsimony method, unweighted, and weighted unifrac metric) .


Libshuff

The following commands will execute the integral form (default) of libshuff (repeat with amino acid files):

mothur > read.dist(phylip=aclB.dist, group=aclB.groups)
mothur > libshuff()


This will ouput two files - .libshuff.coverage and .libshuff.summary. The .summary file is also output to the screen and contains the test statistic and significance of each comparison (truncated here):

      Nucelotide Sequences                                  Amino Acid Sequences
Comparison          dCXYScore	 Significance         Comparison          dCXYScore  Significance
257CP-258CP         0.00168611	 0.7948               257CP-258CP         0.00436709  0.2405
258CP-257CP         0.04406525	 0.0932               258CP-257CP         0.0315775   0.0871
257CP-3Y35          0.00404702	 0.0125               257CP-3Y35          0.0001517   0.6729
258CP-259CP         0.01708675	 0.3331               258CP-259CP         0.01670475  0.6678
259CP-258CP         0.028777	 1                    259CP-258CP         0.009709    1
258CP-260CP         0.046763	 0.0177               258CP-260CP         0.03398125  0.003
....................                                 ....................
3Y35-261CP          0.00232016	 0.0613               3Y35-261CP          0.00082524  <0.0001
263CP-3Y35          0.00089925	 0.9464               263CP-3Y35          0.009615    0.4072
3Y35-263CP          0.01349869	 0.0345               3Y35-263CP          0.00082524  0.6263 


Since we need to apply the Bonferroni correction for multiple comparisons, we will consider a comparison significant if has a significance score <0.0012 (experiment-wide false detection rate of 0.05 divided by 42 comparisons). None of these comparisons have significant corrected p-values.


Parsimony Test

The parsimony method (P-test) tests whether two communities have the same structure based on the number of changes require dto explain the distribution of sequences from each sample in a single phylogenetic tree. The iters option increases the number of randomizations performed and increases the accuracy of the p-value (though the parsimony score is the same regardless of the number of iterations). As always, repeat for the amino acid tree:

mothur > read.tree(tree=aclB.tree, group=aclB.groups)
mothur > parsimony(iters=10000)


This will output a parsimony score and p-value to the screen (also in the .psummary file):

Nucleotide Sequences:
       Tree#	Groups	                                     ParsScore	ParsSig
       1	257CP-258CP-259CP-260CP-261CP-263CP-3Y35	180	0.0229
Amino Acid Sequences:
       Tree#	Groups	                                      ParsScore	ParsSig
       1	257CP-258CP-259CP-260CP-261CP-263CP-3Y35	181	0.0381 


This global test indicates that at least one group in both of the trees has a significantly different structure from the other groups (at a significance threshold of 0.05). Since both of these tests are significant, we can proceed to perform pairwise comparisons on both trees using the same command with the groups option:

mothur > parsimony(groups=all, iters=10000)


This outputs another .psummary file (Note: I had to rename the.psummary files that were previously generated or else this command just overwrote it):

        Nucleotide Tree                                     Amino Acid Tree
Tree#	Groups	    ParsScore	ParsSig             Tree# Groups      ParsScore	ParsSig
1	257CP-258CP	7	0.0569              1	  257CP-258CP	  8	 0.3518
1	257CP-259CP	8	0.5204              1	  257CP-259CP	  7	 0.1543
1	257CP-260CP	8	0.2718              1	  257CP-260CP	  8	 0.2765
1	257CP-261CP	8	0.295               1	  257CP-261CP	  8	 0.3038
1	257CP-263CP	8	0.3785              1	  257CP-263CP	  9	 1
1 	257CP-3Y35	8	0.8587              1	  257CP-3Y35	  6	 0.2048
1	258CP-259CP	26	0.3992              1	  258CP-259CP  	 24      0.113
1	258CP-260CP	33	0.0006              1	  258CP-260CP	 39	 0.0963
1	258CP-261CP	32	0.0016              1	  258CP-261CP	 35	 0.0212
1	258CP-263CP	29	0.006               1	  258CP-263CP	 31	 0.0416
1	258CP-3Y35	12	0.2708              1	  258CP-3Y35	 12	 0.2678
1	259CP-260CP	31	0.9609              1	  259CP-260CP	 28	 0.4962
1	259CP-261CP	25	0.1259              1	  259CP-261CP	 28	 0.6155
1	259CP-263CP	22	0.0474              1	  259CP-263CP	 26	 0.536
1	259CP-3Y35	13	0.862               1	  259CP-3Y35	 12	 0.5504
1	260CP-261CP	46	0.3758              1	  260CP-261CP	 44	 0.1814
1	260CP-263CP	43	0.9174              1	  260CP-263CP	 43	 0.9189
1	260CP-3Y35	12	0.1885              1	  260CP-3Y35	 12	 0.1751
1	261CP-263CP	41	0.872               1	  261CP-263CP	 37	 0.3666
1	261CP-3Y35	13	0.6019              1	  261CP-3Y35	 12	 0.2131
1	263CP-3Y35	13	0.7075              1	  263CP-3Y35	 12	 0.3219

After applying the Bonferroni correction (experiment-wide false detection rate of 0.05 divided by 21 comparisons = corrected p-value of 0.0024), there are two significant pairwise comparisons for the nucleotide tree (258CP-260CP and 258CP-261CP) and none for the amino acid tree.

UniFrac

Unweighted UniFrac

The UniFrac metric uses the amount of unique branch length that can be ascribed to each community as a distance measure and can be used to test whether communities differ significantly with the following command, again with a higher number of iterations:

mothur > read.tree(tree=aclB.tree, group=aclB.groups)
mothur > unifrac.unweighted(iters=10000)


The screen and file output is similar to the output for the P-test:

Nucleotide Tree:
       Tree#	Groups	                                        UWScore	        UWSig
       1	257CP-258CP-259CP-260CP-261CP-263CP-3Y35	0.415773	0.0357 
Amino Acid Tree:
       Tree#	Groups	                                        UWScore	        UWSig
       1	257CP-258CP-259CP-260CP-261CP-263CP-3Y35	0.588883	0.2769


The nucleotide-based test indicates at least one group is significantly different from the others and we can proceed to the pairwise comparisons. The amino acid-based test is not significant, which is not surprising as all of the previous analyses have indicated the communities are more similar on the amino acid level.

          Nucleotide Tree 
Tree#	Groups	        UWScore	        UWSig
1	257CP-258CP	0.437247	0.1908
1	257CP-259CP	0.327507	0.8654
1	257CP-260CP	0.387963	0.5879
1	257CP-261CP	0.378014	0.7214
1	257CP-263CP	0.350265	0.7518
1	257CP-3Y35	0.231719	0.8162
1	258CP-259CP	0.420404	0.1234
1	258CP-260CP	0.4629	      <0.00010
1	258CP-261CP	0.48742	      <0.00010
1	258CP-263CP	0.401742	0.0122
1	258CP-3Y35	0.427424	0.1764
1	259CP-260CP	0.349473	0.6402
1	259CP-261CP	0.36835	        0.4952
1	259CP-263CP	0.344038	0.5617
1	259CP-3Y35	0.366215	0.7326
1	260CP-261CP	0.336167      <0.00010
1	260CP-263CP	0.277011	0.626
1	260CP-3Y35	0.385586	0.5563
1	261CP-263CP	0.325746	0.3023
1	261CP-3Y35	0.386146	0.6026
1	263CP-3Y35	0.312903	0.8308

After Bonferroni correction, 258CP-260CP, 258CP-261CP, and 260CP-261CP are significant.


Weighted UniFrac

The weighted Unifrac metric is similar to the unweighted, except it takes the abundance of sequences into account and weights the branch length accordingly. Execute the unifrac.weighted command (repeat for amino acid tree):

mothur > read.tree(tree=aclB.tree, group=aclB.groups)
mothur > unifrac.weighted(iters=10000)


The following output is in the .wsummary file:

      Nucelotide Tree                                        Amino Acid Tree
Tree#	Groups	        WScore	  WSig                Tree# Groups	 WScore	  WSig
1	257CP-258CP	0.04499   0.6041              1	    257CP-258CP	 0.015071 0.5916
1	257CP-259CP	0.05143	  0.3898              1	    257CP-259CP	 0.018941 0.836
1	257CP-260CP	0.037551  0.7                 1	    257CP-260CP	 0.012156 0.5276
1	257CP-261CP	0.038261  0.6685              1	    257CP-261CP	 0.015509 0.3164
1	257CP-263CP	0.043487  0.5142              1	    257CP-263CP	 0.014489 0.0641
1	257CP-3Y35	0.046472  0.7063              1	    257CP-3Y35   0.014502 0.8643
1	258CP-259CP	0.031981  0.5714              1	    258CP-259CP	 0.019491 0.0678
1	258CP-260CP	0.037285  0.0389              1	    258CP-260CP	 0.01181  0.1001
1	258CP-261CP	0.045175  0.0044              1	    258CP-261CP	 0.014043 0.0325
1	258CP-263CP	0.045247  0.009               1	    258CP-263CP	 0.010643 0.1555
1	258CP-3Y35	0.038226  0.7181              1	    258CP-3Y35	 0.01609  0.3679
1	259CP-260CP	0.03075	  0.3621              1	    259CP-260CP	 0.014382 0.31
1	259CP-261CP	0.040222  0.0469              1	    259CP-261CP	 0.017795 0.1413
1	259CP-263CP	0.044766  0.0265              1	    259CP-263CP	 0.015537 0.117
1	259CP-3Y35	0.037576  0.8265              1	    259CP-3Y35	 0.020867 0.7336
1	260CP-261CP	0.020545  0.6925              1	    260CP-261CP	 0.009803 0.3616
1 	260CP-263CP	0.027441  0.256               1	    260CP-263CP	 0.007813 0.3975
1 	260CP-3Y35	0.042687  0.2694              1	    260CP-3Y35	 0.012929 0.3343
1	261CP-263CP	0.02105	  0.8093              1	    261CP-263CP	 0.008512 0.7995
1	261CP-3Y35	0.049985  0.0668              1	    261CP-3Y35	 0.014564 0.2868
1	263CP-3Y35	0.050252  0.0897              1	    263CP-3Y35	 0.015081 0.0258

None of these comparisons have significant Bonferroni corrected p-values.

More protein coding gene examples

Genetic Diversity and Abundance of Flavobacterial Proteorhodopsin in China Seas